Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-08-24

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Time Nick Message
06:35 sneumann__ joined #bioclipse
07:07 Gpox joined #bioclipse
07:13 CIA-63 bioclipse.qsar: Egon Willighagen master * racbdf75 / plugins/net.bioclipse.qsar/onto​logy/descriptor-algorithms.owl :
07:13 CIA-63 bioclipse.qsar: Added descriptors used by the joelib.qsar plugin
07:13 CIA-63 bioclipse.qsar: Signed-off-by: Ola Spjuth <ola.spjuth@farmbio.uu.se> - http://bit.ly/jHsHC
07:13 CIA-63 bioclipse.qsar: Egon Willighagen master * r083a6fa / plugins/net.bioclipse.qsar/onto​logy/descriptor-algorithms.owl :
07:13 CIA-63 bioclipse.qsar: Added object properties for descriptor algorithm hierarchy
07:13 CIA-63 bioclipse.qsar: Signed-off-by: Ola Spjuth <ola.spjuth@farmbio.uu.se> - http://bit.ly/ltkJK
07:13 egonw joined #bioclipse
07:13 CIA-63 bioclipse.qsar: Egon Willighagen master * r07ebc48 / plugins/net.bioclipse.qsar/onto​logy/descriptor-algorithms.owl :
07:13 CIA-63 bioclipse.qsar: Added HTML microformat stuff for marking the spanned content as SMARTS (fixes #1532)
07:13 CIA-63 bioclipse.qsar: Signed-off-by: Ola Spjuth <ola.spjuth@farmbio.uu.se> - http://bit.ly/S6NLF
07:13 CIA-63 bioclipse.qsar: Egon Willighagen master * r4cee576 / plugins/net.bioclipse.qsar/onto​logy/descriptor-algorithms.owl :
07:13 zarah bug #1532 | http://tinyurl.com/muqeg7
07:13 CIA-63 bioclipse.qsar: Ported to old world descriptor algorithm relations to the new OWL
07:13 CIA-63 bioclipse.qsar: Signed-off-by: Ola Spjuth <ola.spjuth@farmbio.uu.se> - http://bit.ly/b4fvS
07:13 CIA-63 bioclipse.qsar: Egon Willighagen master * r25f0170 / plugins/net.bioclipse.qsar/onto​logy/descriptor-algorithms.owl :
07:13 CIA-63 bioclipse.qsar: Added the LogP descriptor used in JOELib
07:13 CIA-63 bioclipse.qsar: Signed-off-by: Ola Spjuth <ola.spjuth@farmbio.uu.se> - http://bit.ly/1adSGb
07:14 CIA-63 bioclipse.qsar: Egon Willighagen master * re084d70 / plugins/net.bioclipse.qsar/onto​logy/descriptor-algorithms.owl :
07:14 CIA-63 bioclipse.qsar: Fixed a typo: I'm positive the rotatableCount descriptors counts the rotatable bonds, not the non-rotable bonds
07:14 CIA-63 bioclipse.qsar: Signed-off-by: Ola Spjuth <ola.spjuth@farmbio.uu.se> - http://bit.ly/MhPen
07:14 CIA-63 bioclipse.qsar: Egon Willighagen master * r86ba517 / plugins/net.bioclipse.qsar/onto​logy/descriptor-algorithms.owl :
07:14 CIA-63 bioclipse.qsar: Fixed typo in XML syntax
07:14 CIA-63 bioclipse.qsar: Signed-off-by: Ola Spjuth <ola.spjuth@farmbio.uu.se> - http://bit.ly/y5zgV
07:15 olass joined #bioclipse
07:16 egonw moin
07:16 zarah hi egonw
07:17 egonw olass: skype when jonathan gets online?
07:18 olass egonw: sure. What is the urgent matter?
07:18 egonw structuredb
07:18 olass ok
07:38 CIA-63 bioclipse.qsar: Ola Spjuth master * red3772e / (2 files in 2 dirs): Use same preferences as FieldEditor does for preferred descriptor provider order. - http://bit.ly/4FaLNL
07:38 CIA-63 bioclipse.qsar: Ola Spjuth master * r5a754c5 / plugins/net.bioclipse.qsar/src/net/bio​clipse/qsar/business/QsarManager.java : NPE check for no results when storing results. - http://bit.ly/4wqtEb
07:38 CIA-63 bioclipse.qsar: Ola Spjuth master * r87ebe0f / plugins/net.bioclipse.qsar.ui/src/net/bi​oclipse/qsar/ui/builder/QSARBuilder.java : If error in descriptor result, do not try to store it. - http://bit.ly/KMHZ4
07:38 CIA-63 bioclipse.qsar: Ola Spjuth master * r263869e / plugins/net.bioclipse.cdk.qsar.xmpp/src/net/biocli​pse/cdk/qsar/xmpp/CdkXMPPDescriptorCalculator.java : Continued working on parsing of XMPP results but hit the wall. Bug 1547 filed for egonw. - http://bit.ly/PQeqB
07:38 zarah bug #1547 | http://tinyurl.com/nmuz7f
07:38 CIA-63 bioclipse.qsar: Ola Spjuth master * r5139ef9 / (4 files in 4 dirs): Merge branch 'local' - http://bit.ly/DPnrr
07:39 olass hmm, i di rebase
07:39 olass must have messed something up
07:39 olass whateve
07:39 egonw ah, it happens
07:39 egonw to me too now and then
07:40 egonw will try to solve the CML parsing in JOELib today
07:40 olass egonw: please see my bug 1547
07:40 egonw it's throwing a Xerces class not found
07:40 egonw @pz 1547
07:40 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1547
07:40 olass egonw: oh, you have the same in joelib?
07:40 egonw yes, you too somewhere?
07:40 olass I just filed CML parsing as a bug in XMPP :)
07:40 olass sound like to flies in one go for you :)
07:40 olass two
07:41 egonw is that a CNF too?
07:41 egonw or some other problem?
07:41 olass no idea
07:41 olass what is CNF?
07:46 CIA-63 bioclipse: ospjuth * r11725 /bioclipse2/trunk/plugins/net.bioclipse.​xws4j/src/net/bioclipse/xws4j/views/serv​icediscovery/ServiceDiscoveryView.java: Make sure serviceDiscView is open if update labels. Also remove listeners on dispose(). Solves annoying NPE if ServiceDiscView is opened and then closed.
07:57 egonw ClassNotFound
07:57 olass ah
07:57 egonw just made that up
07:57 olass Common Navigator Framework too :)
07:58 * egonw is gonna make coffee
07:58 * olass too
08:03 mgerlich joined #bioclipse
08:07 shk3 joined #bioclipse
08:24 olass egonw: ping
08:25 egonw pong
08:25 olass we now only list the following categories: constitutional, electronic, geometrical, and topological
08:25 olass BCUT is classified as hybridDescriptor only
08:25 olass I think that is why it does not show up
08:25 egonw ah, ic
08:25 egonw mmm...
08:25 olass so
08:25 egonw so, why does hybrid not show up
08:26 egonw will look at the ontology
08:26 olass please do
08:26 egonw stupid I did not think of that
08:26 egonw please reassign bug
08:26 olass well, we now have a chack for this in the QSAR plugin
08:26 olass it logs impl that does not find a BODO ref
08:26 olass ok
08:27 olass egonw: same is WHIM
08:27 egonw ack
08:27 egonw should not be too difficult to fix
08:29 olass egonw: is there a bug for joelib parsing?
08:30 * olass has hadded bug 1550 as container for QSAR 2.1.1 release
08:32 masak joined #bioclipse
08:32 olass egonw: please comment on my comment on bug 1545
08:32 masak o/
08:32 olass \o
08:37 egonw ack on 1550
08:39 olass @pz partition
08:39 zarah olass: Zarro boogs found.
08:39 olass @pz fragmentate
08:39 zarah olass: Zarro boogs found.
08:43 egonw just organizing his todo list is a day job for egonw
08:50 olass egonw: I'd like to request from you to close the bugs that you reported and which are marked as RESOLVED. Bug 794 is one example.
08:50 edrin joined #bioclipse
08:50 olass 795 as well
08:50 edrin left #bioclipse
08:50 edrin joined #bioclipse
08:51 egonw ah, good one
08:51 egonw I used to have a Mylyn category for tha...
08:51 egonw will make one again...
08:51 edrin hi
08:51 zarah ni hao edrin
08:51 egonw olass: and there are *many* more
08:51 egonw hi edrin!
08:53 olass hi edrin
08:53 jonalv joined #bioclipse
08:54 egonw hi jonalv!
08:54 egonw you fantastic person!
08:54 olass o/
08:55 jonalv hello
08:55 zarah privet jonalv
08:56 jonalv how's everyone today?
08:57 olass jonalv: alive and kicking
09:03 * masak feels alive and kicked
09:10 egonw masak: :)
09:11 olass to clarify: I did *not* kick masak
09:11 * egonw has 74 RESOLVED bugs who he needs checking :(
09:11 masak olass: :)
09:11 egonw olass: you just asked some bloke ?
09:11 masak egonw: but that's the fun part, right?
09:11 egonw it's all in the semantics
09:11 masak egonw: getting to check that things have gotten better.
09:11 egonw yeah, indeed!
09:12 egonw that's why I haven't been doing it in months!
09:12 egonw :)
09:12 masak ...saving it up...
10:06 egonw shk3: can I search nmrshiftdb for structures with spectra which are retrieved from a particular paper?
10:07 shk3 yes
10:07 shk3 search by author or paper title
10:07 egonw spectrum property -> Literature/Author ?
10:07 shk3 yes
10:07 egonw thanx
10:08 shk3 or Literature/Title
10:08 egonw oh...
10:08 egonw ok... I read that '/' as 'or'
10:08 shk3 no - it's sort of subcategory
10:09 shk3 perhaps a bit misleading
10:09 egonw perhaps "Literature: Author" ?
10:09 egonw ummm
10:09 egonw I'm now stuck
10:09 egonw I had selected Literature/Author
10:09 egonw and now it no longer shows up all options...
10:09 egonw only four
10:09 shk3 that sounds like you left export mode
10:10 egonw and can't find how to reset it...
10:10 shk3 switch back
10:10 egonw ah, indeed
10:10 shk3 not sure how this happened
10:10 egonw had not noticed that
10:11 egonw btw, should I try submitting new spectra with speclipse again?
10:11 shk3 no sorry
10:12 egonw olass: is the R Console part of bioclipse.core ?
10:12 shk3 still stuck with that
10:12 egonw olass: should it?
10:12 shk3 it's a reproducable jvm error
10:12 egonw olass: masak gave me a nice demo last week
10:12 shk3 I will try out with other jvm versions, right now this is the only idea I have what I can do at all
10:12 shk3 it's really nasty
10:13 olass egonw: R console is part of experimental
10:13 olass as it should be
10:13 egonw yeah, because input via the website is so much time consuming than speclipse
10:13 egonw olass: ack
10:14 egonw masak: got that? it's part of bioclipse.experimental
10:14 masak egonw: that explains things.
10:14 masak egonw++ # so it wasn't something you accidentally removed
10:15 egonw shk3: ack, will see if I can do a bit via the website then
10:15 olass masak: how is biojava and the sequence editor coming along btw? anything new I can try?
10:15 * olass is curious
10:15 masak olass: I'm in the process of adding more manager methods.
10:15 masak @pz 1452
10:15 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1452
10:15 olass masak: ack
10:49 olass is it possible to update the status of several bugs at the same time in bugzilla?
10:49 olass I want to set 2.1 -> 2.2 for 20 bugs...
10:49 olass anyone?
10:50 masak olass: not that I know of.
10:50 olass SF had that..
10:50 olass "mass update"
10:50 olass very useful
10:50 masak sounds like a perfect job for a mechanized web client, though.
10:51 masak ...or just dive into the database itself and do an update. :)
10:51 olass right
10:53 olass ah, found it :)
10:54 jonalv masak: why do you hate user interfaces?
10:54 masak jonalv: *lol*
10:54 masak "why do you hate America?"
10:56 jonalv because they hate you back
10:56 jonalv ?
10:58 masak I don't hate user interfaces. they're needed to communicate with our computer hardware. if we didn't have user interfaces, computers would just be big black boxes, just sitting there. (that was what it was like in the early 50s)
10:58 masak hating user interfaces seems a quite silly thing to do.
10:59 jonalv masak: oh you know what I mean
10:59 masak I do. but I still think the question is unjust.
11:01 jonalv good
11:04 egonw olass: use the web interface
11:04 egonw do the proper search
11:04 egonw then down the bottom there should be along the lines of mass update
11:04 masak egonw++
11:04 egonw shk3: is there a RSS feed of ones NMRShiftDB contributions?
11:04 olass egonw: [12:53] < olass> ah, found it :)
11:05 egonw shk3: if not, please consider that as a feature request
11:05 egonw oh, missed that
11:06 egonw shk3: another thing...
11:06 masak lunch &
11:06 egonw I just submitted 6 H2O spectra (various solvents), but they do not show up in unreviewed on my homepage
11:06 shk3 I think they will
11:07 shk3 not sure if you noticed, but a while ago i changed stuff
11:07 shk3 submits are no longer written to db directly,
11:07 shk3 but in the background
11:07 shk3 so it can take a while
11:07 egonw shk3: ah, ic. I had not noticed until just now :)
11:08 egonw should I file that RSS feature request ?
11:09 shk3 yes
11:09 shk3 please
11:14 CIA-63 bioclipse.qsar: Ola Spjuth master * ra799075 / (3 files in 2 dirs): Added check to log descriptor implementations that do not connect to a visible ontology entry. - http://bit.ly/XL4gF
11:17 shk3 Gpox: around?
11:17 Gpox yes
11:18 shk3 I filed several bug reports all relating to jcp and starting with drawing a single atom
11:18 shk3 right now, this seems not to work at all
11:18 shk3 I get the impression the whole initialization/setup
11:19 shk3 is seriously broken when starting with an atom
11:19 shk3 it looks ok when starting with a ring
11:19 egonw shk3: ask how Gpox does it..
11:19 egonw it works in Bioclipse
11:19 shk3 as I said, it's several bugs, but the underlying problem might be the same
11:20 shk3 what works in bioclipse?
11:20 egonw but this why this split up of renderers for IAtomContainer and IChemModel is so interesting, I think
11:20 egonw makes it more clear what the data model is
11:20 egonw drawing a first (single) atom
11:20 shk3 not working for me
11:20 shk3 it used to do,
11:21 shk3 but even then there were problems when you wanted to continue
11:21 shk3 please have a look at the bug reports if you are unsure
11:21 egonw Gpox: can you please?
11:21 shk3 I don't think it's related to this splitup or whatever
11:21 Gpox there was some change
11:21 shk3 but I am not going to discuss this
11:21 shk3 look at bug reports and try it out, please
11:22 Gpox to the setup it might have broken something
11:22 shk3 might be
11:22 shk3 not sure
11:22 shk3 it just looks like a serious problem influencing lots of stuff
11:22 shk3 I wanted to make you aware of that
11:24 egonw Gpox: do you know what patch made that change? if so, please comment that in the bug report
12:35 masak olass: do you know how to convert from protein to DNA using Biojava?
12:36 olass nope
12:36 olass did that exist in bc1?
12:36 masak dunno.
12:36 olass have a look
12:36 * masak looks
12:36 olass I seem to remember it existed
12:36 olass and that it was non-trivial
12:38 masak right now, that doesn't surprise me.
12:55 egonw shk3: ping
12:56 shk3 yes
12:56 egonw getting back on the water spectra submissions...
12:56 egonw I just received an email that my latest aceton is sent for review
12:57 egonw but never got such emails for the 6 water spectra I submitted...
12:57 shk3 mom
12:58 masak uncle!
12:59 shk3 still to be processed, it seems
12:59 egonw oh... they are not processed in the same order as they were submitted?
12:59 egonw ok, will be more patient then...
13:00 shk3 probably not
13:00 shk3 order is probably random
13:00 shk3 didn't really care about it
13:00 egonw yeah, it's fine...
13:00 egonw I was still used to the old way
13:00 egonw where things were processed as they came in
15:21 * masak reads http://wiki.bioclipse.net/index.p​hp?title=How_to_make_a_manager_2
15:21 masak how much MediaWiki's search function sucks is really a mystery to me.
15:22 masak I search for 'manager 2' and that page comes up as hit number #5. how is that possible?
15:26 egonw yeah, got my google wave invite!
15:26 edrin egonw: what is a google wave invite?
15:26 egonw just google for 'google wave'
15:26 olass egonw: I wish I was as glad as you for every new technology
15:26 egonw and watch the movie
15:27 olass :)
15:28 olass egonw: will we see a Google Wave plugin for Bioclipse soon?
15:28 olass and what can we do with it?
15:28 egonw not before the IO-DATA plugin
15:28 egonw wave is build on top of XMPP too
15:28 olass ok
15:28 egonw edrin: I think you will quite like it
15:34 edrin ah right
15:35 * masak rolls eyes
15:35 masak google wave, google schmave. :P
15:35 zarah masak: http://www.everythingicafe.com/for​um/archive/index.php/t-41519.html
15:35 masak *lol*
15:36 jonalv google is the new black
15:36 zarah jonalv: http://en.wikipedia.org/wiki/The_new_black
15:36 masak I think that's the most useless accidental search I've ever done.
15:37 jonalv hehe
17:03 CIA-63 bioclipse.qsar: Ola Spjuth master * rc183486 / (2 files in 2 dirs): Added a QSAR perspective. Solves 1554. - http://bit.ly/3XZzR5
17:32 sneumann__ joined #bioclipse
17:49 CIA-63 bioclipse.core: Carl Masak master * rc8f9a31 / (37 files in 18 dirs):
17:49 CIA-63 bioclipse.core: changed 'Javascript' -> 'JavaScript' everywhere
17:49 CIA-63 bioclipse.core: Some changes involved 'Javascripts' -> 'JavaScript scripts' too. It was
17:49 CIA-63 bioclipse.core: all horribly confused. Hopefully a little better now. - http://bit.ly/s2Tg6
18:19 CIA-63 bioclipse.qsar: Ola Spjuth master * r893dbbb / (13 files in 5 dirs): A lot of documentation for the QSAR feature. - http://bit.ly/4aVv6
18:21 edrin left #bioclipse
19:37 sneumann joined #bioclipse
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20:04 egonw joined #bioclipse
20:57 CIA-63 bioclipse.core: Egon Willighagen master * r36f2217 / plugins/net.bioclipse.busi​ness/META-INF/MANIFEST.MF : Fixed Bundle name - http://bit.ly/HCMNB
20:57 CIA-63 bioclipse.core: Egon Willighagen master * ra19cc08 / (2 files): Added two download methods to give a String and a IFile (implements #1541) - http://bit.ly/qmLwM

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